Zinc in PDB 7bj8: Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B

All present enzymatic activity of Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B:
3.5.2.6;

The structure of Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B, PDB code: 7bj8 was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.60 / 1.69
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.2, 105.2, 97.96, 90, 90, 120
R / Rfree (%)	16.3 / 18.9

The binding sites of Zinc atom in the Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B (pdb code 7bj8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B, PDB code: 7bj8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.5 occ:1.00 H18 A:QST301 2.0 34.2 0.9 NE2 A:HIS225 2.0 21.5 1.0 OD2 A:ASP88 2.0 21.2 1.0 NE2 A:HIS89 2.0 20.0 1.0 S01 A:QST301 2.2 28.5 0.9 CG A:ASP88 2.8 33.0 1.0 H2 A:QST301 2.9 45.2 0.9 CE1 A:HIS225 2.9 23.1 1.0 OD1 A:ASP88 3.0 20.3 1.0 CE1 A:HIS89 3.0 23.2 1.0 CD2 A:HIS89 3.0 22.9 1.0 CD2 A:HIS225 3.0 22.0 1.0 HE1 A:HIS225 3.1 27.7 1.0 C02 A:QST301 3.1 37.7 0.9 HE1 A:HIS89 3.2 27.9 1.0 HD2 A:HIS89 3.2 27.4 1.0 HD2 A:HIS225 3.3 26.5 1.0 S09 A:QST301 3.6 48.2 0.9 ZN A:ZN303 3.9 20.2 1.0 H11 A:QST301 3.9 57.7 0.9 C03 A:QST301 3.9 45.8 0.9 H1 A:QST301 3.9 45.2 0.9 HE1 A:HIS84 3.9 20.5 1.0 ND1 A:HIS225 4.1 22.5 1.0 ND1 A:HIS89 4.1 19.2 1.0 CG A:HIS89 4.1 20.0 1.0 CG A:HIS225 4.1 21.7 1.0 CB A:ASP88 4.2 17.4 1.0 HG A:SER185 4.2 33.3 1.0 HB2 A:ASP88 4.2 20.9 1.0 O A:HOH411 4.3 31.1 1.0 H12 A:QST301 4.3 57.7 0.9 NE2 A:HIS84 4.4 16.2 1.0 N17 A:QST301 4.4 47.6 0.9 CE1 A:HIS84 4.5 17.1 1.0 C12 A:QST301 4.5 48.1 0.9 HZ3 A:TRP17 4.6 28.3 1.0 HD21 A:LEU38 4.6 26.3 1.0 HB3 A:ASP88 4.7 20.9 1.0 HB2 A:HIS86 4.7 19.7 1.0 HH2 A:TRP17 4.7 28.2 1.0 C10 A:QST301 4.8 47.7 0.9 HD22 A:LEU38 4.8 26.3 1.0 HD1 A:HIS225 4.8 27.1 1.0 HD1 A:HIS89 4.8 23.0 1.0 HB2 A:PRO224 4.9 22.4 1.0 H A:ASP88 4.9 21.0 1.0 OG A:SER185 4.9 27.7 1.0 CZ3 A:TRP17 5.0 23.6 1.0

Zinc binding site 2 out of 2 in the Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of L1 with 2-Mercaptomethyl-Thiazolidine D-Syn-1B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:20.2 occ:1.00 H18 A:QST301 1.9 34.2 0.9 NE2 A:HIS84 2.0 16.2 1.0 NE2 A:HIS160 2.0 19.6 1.0 ND1 A:HIS86 2.1 19.1 1.0 S01 A:QST301 2.3 28.5 0.9 CD2 A:HIS160 2.9 19.9 1.0 CE1 A:HIS86 2.9 19.1 1.0 CD2 A:HIS84 3.0 17.6 1.0 CE1 A:HIS84 3.0 17.1 1.0 HD2 A:HIS160 3.0 23.9 1.0 H1 A:QST301 3.1 45.2 0.9 HB2 A:HIS86 3.1 19.7 1.0 HE1 A:HIS86 3.1 23.0 1.0 CE1 A:HIS160 3.1 22.6 1.0 CG A:HIS86 3.1 18.3 1.0 HD2 A:HIS84 3.2 21.1 1.0 HE1 A:HIS84 3.2 20.5 1.0 C02 A:QST301 3.3 37.7 0.9 HE1 A:HIS160 3.4 27.1 1.0 CB A:HIS86 3.5 16.4 1.0 HD2 A:HIS89 3.6 27.4 1.0 HB3 A:HIS86 3.8 19.7 1.0 ZN A:ZN302 3.9 23.5 1.0 H2 A:QST301 3.9 45.2 0.9 ND1 A:HIS84 4.0 19.4 1.0 CG A:HIS84 4.1 16.5 1.0 NE2 A:HIS86 4.1 16.8 1.0 CG A:HIS160 4.1 18.7 1.0 ND1 A:HIS160 4.2 20.7 1.0 CD2 A:HIS86 4.2 19.5 1.0 HG A:SER185 4.2 33.3 1.0 CD2 A:HIS89 4.2 22.9 1.0 HE2 A:PHE124 4.3 58.4 1.0 OD1 A:ASP88 4.3 20.3 1.0 NE2 A:HIS89 4.4 20.0 1.0 C03 A:QST301 4.4 45.8 0.9 N17 A:QST301 4.4 47.6 0.9 HG23 A:THR161 4.4 18.5 1.0 H15 A:QST301 4.4 57.1 0.9 HB2 A:SER185 4.7 27.6 1.0 O A:HOH411 4.8 31.1 1.0 HD1 A:HIS84 4.8 23.4 1.0 H A:HIS86 4.8 19.9 1.0 HE2 A:HIS86 4.9 20.2 1.0 OG A:SER185 4.9 27.7 1.0 CA A:HIS86 5.0 15.8 1.0 HZ A:PHE124 5.0 51.0 1.0 HD1 A:HIS160 5.0 24.8 1.0

P.Hinchliffe, D.M.Moreno, M.A.Rossi, M.F.Mojica, V.Martinez, V.Villamil, B.Spellberg, G.L.Drusano, C.Banchio, G.Mahler, R.A.Bonomo, A.J.Vila, J.Spencer. 2-Mercaptomethyl Thiazolidines (Mmtzs) Inhibit All Metallo-Beta-Lactamase Classes By Maintaining A Conserved Binding Mode. Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
PubMed: 34355567
DOI: 10.1021/ACSINFECDIS.1C00194